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On a cruise to Bermuda in 2007, Baltimore resident Wilhelmina Watnoski was surprised to find that passengers were required to clean their hands when entering and leaving the ship’s eatery. “There was actually a person standing there making you do it,” Watnoski recalls. Her reaction? A note of thanks to the ship’s management.

Watnoski is all too aware of the destruction a tiny, unseen germ can wreak. Two of the most dangerous and most common bugs that stalk U.S. health care facilities infected her 80-year-old father in late 2004 after he was hospitalized for a urinary tract infection. Sent to a rehabilitation facility to regain his strength, Walter Wiatr instead developed uncontrollable diarrhea and lost his appetite. That, Watnoski learned, was thanks to an organism called Clostridium difficile (C. diff). She moved him to another facility. But soon a painful red swelling appeared on his neck, the sign of another infection—this time it was methicillin-resistant Staphylococcus aureus, or MRSA, a bacterium that’s spread by person-to-person contact and is resistant to common antibiotics. Two months after his initial hospitalization, Wiatr, who’d been independent and healthy, was gone.

“He went downhill so fast, I still can’t believe it happened like that,” his daughter says.

American hospitals are treating sicker patients with more complex, invasive techniques—and helping people live longer. But every year in these same facilities some 90,000 Americans pick up infections that kill them.

Hard-to-treat superbugs are an increasing problem as widespread use of antibiotics produces new germs that are drug-resistant—and few new medications are in the pipeline. In the 1970s only a tiny percentage of hospital staph infections were MRSA. By 2004 MRSA accounted for two out of three staph infections, usually attacking patients with weakened immune systems or those using catheters, intravenous lines or ventilators.

Clostridium difficile also is a rising threat. Few Americans had heard of this intestinal bug until November, when a study showed its prevalence is as much as 20 times higher than previous estimates. Sponsored by the Association for Professionals in Infection Control and Epidemiology (APIC), the study looked at C. diff cases in nearly 650 U.S. health care facilities on a single day between May and August 2008. Findings suggest that on an average day, nearly 7,200 hospitalized patients—13 of every 1,000—are colonized or, more often, infected with C. diff, and about 300 patients will not survive it. The young and older patients are especially vulnerable. Infection often follows the use of antibiotics, which strip the gut of certain bacteria, allowing C. diff to proliferate there.

Research has shown that health care workers clean their hands effectively only about half the time, and the hardiness of the C. diff spores adds a twist to the challenges they face. At one time the U.S. Centers for Disease Control and Prevention (CDC) routinely recommended cleaning the hands with alcohol-based rubs. But alcohol won’t kill C. diff—it takes a scrubbing with soap and warm water to eliminate the spores. Similarly, only bleach will kill spores on surfaces; but the APIC study found that even in an outbreak, about a third of institutions don’t clean with bleach.